First off, the way the Duty finder and 'Data Center' system works, makes it so being on a low pop. server really, overall, isn't that big of an issue. Since the Duty Finder randomly matches you with people linked in your Data Center...and since each Data center has a mix of High/Mid/Low pop servers, your wait times aren't super long etc just because less people live on your server.

Sure, if you're a hard-core 'world first' raider type, you might have trouble finding others for cutting edge content on a low pop server, but that is actually a fairly unique situation (overall) for most people...and even then, finding 7 other people isn't that hard...as even a 'low pop' server in this game (unless it's brand new) actually doesn't mean 'ghost town.

Furthermore, there are perks to being on a lower population server (I left a high pop for a mid sized so I have some reference on the matter).

1. You likely can buy a house...AND it's likely to be cheaper than the same house/plot on a larger pop server.
2. Hunts aren't a complete zerg/disappear from my screen/scream at each other fest.
3. People tend to be more helpful to strangers (because 1. you need to help eachother and 2. lower pop means it's easier to remember names and if you develop a bad rep it'll cost you.
4. At least in my case, your gil is worth more, buying power is more and the markets are more stable on a lower pop. server. This might just be my experience...and likely best on Mid-sized servers (which I believe I am on). As low pop might not have enough ebb/flow on the MB's but High pop has too much.
5. Some people like 'quieter'. Not all mind you, but some people find it nice to be out gathering and maybe only see a couple people in passing...others would find that maddening. Depends on who you are.
6. On Launch Days/Patch days... you stand a shot of logging in even if you didn't attempt to get online the moment the servers go live. It's nice to be able to sleep, and log in at your leisure.

Boils down to something as simple really as 'why do some people like living in the city vs. some in the country' Both have pros and cons.